21 Works

The Pacific lamprey genomic divergence, association mapping, temporal Willamette Falls, spatial rangewide datasets

Jon Hess, Jeramiah Smith, Nataliya Timoshevskaya, Cyndi Baker, Christopher Caudill, David Graves, Matthew Keefer, Andrew Kinziger, Mary Moser, Laurie Porter, Greg Silver, Steven Whitlock & Shawn Narum
High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome...

The skin microbiome facilitates adaptive tetrodotoxin production in poisonous newts

Patric Vaelli, Kevin Theis, Janet Williams, James Foster, Lauren O'Connell & Heather Eisthen
Rough-skinned newts (Taricha granulosa) use tetrodotoxin (TTX) to block voltage-gated sodium (Nav) channels as a chemical defense against predation. Interestingly, newts exhibit extreme population-level variation in toxicity attributed to a coevolutionary arms race with TTX-resistant predatory snakes, but the source of TTX in newts is unknown. Here, we investigated whether symbiotic bacteria isolated from toxic newts could produce TTX. We characterized the skin-associated microbiota from a toxic and non-toxic population of newts and established pure...

Allometric modelling of plant biomass from drone-acquired photographs: drone images, ground control marker coordinates and biomass data from 36 sites, 2016-2020

A. Cunliffe, K. Anderson, F. Boschetti, H. Graham, R. Brazier, I. Myers-Smith, T. Astor, M. Boer, L. Calvo, P. Clark, M. Cramer, M. Encinas-Lara, S. Escarzaga, J. Fernández-Guisuraga, A. Fisher, K. Gdulová, B. Gillespie, A. Griebel, N. Hanan, M. Hanggito, S. Haselberger, C. Havrilla, W. Ji, J. Karl, M. Kirchhoff … & R. Wojcikiewicz
This dataset contains RGB photographs acquired from drone surveys. There are 741 harvest plots from 38 surveys at 36 sites around the world. Each site was approximately 1 ha in area. Included with the photographic images are the coordinates of ground control markers, biomass, taxonomic and location data for harvest plots and ancillary metadata. The observations can be used to obtain allometric size-biomass models. This work was supported by the Natural Environment Research Council award...

Water Balance Model (WBM) simulations of the Upper Snake River Basin 2008-2017

Shan Zuidema

Scripts from: Controlling evolution in genetically engineered systems through repeated introduction

Nathan Layman
Genetically engineered transgenes evolve in the same way as other genetic material. However, evolution in engineered genes is often undesirable and can negatively affect their stability, frequency, and efficacy over time. Methods that maintain the stability of engineered genomes are therefore critical to the successful design and use of genetically engineered organisms. One potential method to limit unwanted evolution is by taking advantage of the ability of gene-flow to counter local adaption, a process of...

Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Jelmer Poelstra, Jordi Salmona, George Tiley, Dominik Schüßler, Marina Blanco, Jean Andriambeloson, Olivier Bouchez, C. Ryan Campbell, Paul Etter, Amaia Iribar-Pelozuelo, Paul Hohenlohe, Kelsie Hunnicutt, Eric Johnson, Peter Kappeler, Peter Larsen, Sophie Manzi, Jose Ralison, Blanchard Randrianambinina, Rodin Rasoloarison, David Rasolofoson, Amanda Stahlke, David Weisrock, Rachel Williams, Lounes Chikhi, Ed Louis … & Anne Yoder
Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, especially when undescribed lineages may be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of a rapid radiation of morphologically cryptic species that are distributed throughout Madagascar in its rapidly vanishing forested habitats. Here, we focus on two pairs of sister lineages that occur in a region in northeastern Madagascar that shows high levels of microendemism. We...

Data from: Long-lived marine species may be resilient to environmental variability through a temporal portfolio effect

Jacek Maselko, Kimberly Andrews & Paul Hohenlohe
Maintenance of a portfolio of adaptive alleles may provide resilience of populations to natural environmental variability. We used Pacific ocean perch (POP; Sebastes alutus) to test for the maintenance of adaptive variation across overlapping generations. POP are a long-lived species characterized by widespread larval dispersal in their first year and a longevity of over 100 years. In order to understand how early marine dispersal affects POP survival and population structure, we used Restriction Site Associated...

Data from: Anatomical and hydraulic responses to desiccation in emergent conifer seedlings

Daniel Johnson, Megan Miller, Adam Roddy, Craig Brodersen & Andrew McElrone
Premise of the study: The young seedling life stage is critical for reforestation after disturbance and for species migration under climate change, yet little is known regarding their basic hydraulic function or vulnerability to drought. Here, we sought to characterize responses to desiccation including hydraulic vulnerability, xylem anatomical traits, and impacts on other stem tissues that contribute to hydraulic functioning. Methods: Larix occidentalis , Pseudotsuga menziesii , and Pinus ponderosa (all < 6 weeks-old) were...

Direction and magnitude of natural selection on body size differs among age classes of seaward migrating Pacific salmon

Marta Ulaski, Heather Finkle & Peter Westley
Due to the mediating role of body size in determining fitness, the ‘bigger is better’ hypothesis still pervades evolutionary ecology despite evidence that natural selection on phenotypic traits varies in time and space. For Pacific salmon (genus Oncorhynchus), most individual studies quantify selection across a narrow range of sizes and ages; therefore, uncertainties remain concerning how selection on size may differ among diverse life-histories. Here, we quantify the direction and magnitude of natural selection on...

Tag, migration, and fate data of adult radio-tagged Chinook and sockeye salmon and steelhead in the Columbia River Basin 1996-2014

Matthew Keefer, Michael Jepson, Christopher Caudill & Tami Clabough
These datasets provide information on radiotelemetry tagging, migration and fate of adult spring, summer, and fall Chinook salmon (Oncorhynchus tshawytscha), sockeye salmon (O. nerka) and steelhead (O. mykiss) in the Columbia River Basin, 1996-2014. The tagging database provides tagging metrics that include date collected at time of capture and release, size, fin clips, condition, injuries, marks or tags, release site, etc. The migration databases includes complete migration histories and integrates all coded radio detections, PIT-tag...

Data from: Predicting fine root lifespan from plant functional traits in temperate trees

M. Luke McCormack, Thomas S. Adams, Mark D. Coleman & David M. Eissenstat
• Although linkages of leaf and whole-plant traits to leaf lifespan have been rigorously investigated, there is a limited understanding of similar linkages of whole-plant and fine root traits to root lifespan. In comparisons across species, do suites of traits found in leaves also exist for roots, and can these traits be used to predict root lifespan? • We observed the fine root lifespan of 12 temperate tree species using minirhizotrons in a common garden...

Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

Jack Sullivan & Brice Sarver
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North...

Code and scripts used to generate results for: Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency

Nathan Layman, Beth Tuschhoff & Scott Nuismer
The danger posed by infectious agents necessitates the development of new tools to both predict and manage emerging diseases. One promising approach is the development of recombinant viral vaccines that are themselves infectious. Transmissible vaccines have been shown to greatly reduce the effort required to control the spread of zoonotic pathogens in their animal reservoirs, thereby limiting the chances of human infection. While this approach can be immensely useful in combating emerging diseases, the ability...

Data from: Diet of a rare herbivore based on DNA metabarcoding of feces: selection, seasonality, and survival

Amanda Goldberg, Courtney Conway, David Tank, Kimberly Andrews, Digpal Gour & Lisette Waits
In herbivores, survival and reproduction are influenced by quality and quantity of forage and, hence, diet and foraging behavior are the foundation of an herbivore’s life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: 1) they are difficult...

Data from: Primers to highly conserved elements optimized for qPCR-based telomere length measurements in vertebrates

Stephanie Hudon, Esteban Palencia Hurtado, James Beck, Steven Burden, Devin Bendixsen, Kathleen Callery, Jennifer Sorensen Forbey, Lisette Waits, Robert Miller, Ólafur Nielsen, Julie Heath & Eric Hayden
Telomere length dynamics are an established biomarker of health and aging in animals. The study of telomeres in numerous species has been facilitated by methods to measure telomere length by real-time quantitative PCR (qPCR). In this method, telomere length is determined by quantifying the amount of telomeric DNA repeats in a sample and normalizing this to the total amount of genomic DNA. This normalization requires the development of genomic reference primers suitable for qPCR, which...

Data and R Source Code for \"Toward a Novel Laser-Based Approach for Estimating Snow Interception\"

Micah Russell
The primary objective of this study was to provide a feasibility assessment for estimating snow interception volume with terrestrial laser scanning (TLS), providing information on challenges and opportunities for future research. During the winters of 2017 and 2018, intercepted snow masses were continuously measured for two model trees suspended from load-cells. Simultaneously, autonomous terrestrial lidar scanning (ATLS) was used to develop volumetric estimates of intercepted snow.

Data from: Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations

Alexandra Kaye Fraik, Mark Margres, Brendan Epstein, Soraia Barbosa, Menna Jones, Sarah Hendricks, Barbara Schonfeld, Amanda R. Stahlke, Anne Veillet, Rodrigo Hamede, Hamish McCallum, Elisa Lopez-Contreras, Samantha J Kallinen, Paul A Hohenlohe, Joanna Kelley & Andrew Storfer
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors such as disease. The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a nearly 100% fatal, transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species’ extinction, suggesting possible adaptation to...

Data from: Converting conventional agriculture to poplar bioenergy crops: soil chemistry

Mark Coleman & A. Mukherjee
Woody bioenergy is a viable source of alternative energy; however, questions remain on how purpose-grown bioenergy feedstock production management impact surface soil chemistry. In order to understand the soil processes under poplar (Populus spp.) trees and adjacent agricultural sites, surface (0-15 cm) soil samples were collected from four northwestern United States locations over a four-year period. Initial and final surface soil samples were analyzed for various soil chemical parameters, including organic matter, pH, cation exchange...

Data on universities offering undergraduate degrees that train students for soil science careers at universities in the USA and its territories

Eric C. Brevik, Holly Dolliver, Susan Edinger-Marshall, Danny Itkin, Jodi Johnson-Maynard, Garrett Liles, Monday Mbila, Colby Moorberg, Yaniria Sanchez-De Leon, Joshua J. Steffan, April Ulery & Karen Vaughan
Several soil science education studies over the last 15 years have focused on the number of students enrolled in soil science programs. However, no studies have quantitatively addressed the number of undergraduate soil science preparatory programs that exist in the United States, which means we do not have solid data concerning whether overall program numbers are declining, rising, or holding steady. This also means we do not have complete data on the same trends for...

Thermal tolerance and cardiac phenotypes

Zhongqi Chen
Adaptation to local environments involves the evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific...

Thermal constraints on energy balance, behavior, and spatial distribution of grizzly bears

Savannah Rogers, Charles Robbins, Paul Mathewson, Anthony Carnahan, Frank Van Manen, Mark Haroldson, Warren Porter, Taylor Rogers, Terence Soule & Ryan Long
1. Heat dissipation limit theory posits that energy available for growth and reproduction in endotherms is limited by their ability to dissipate heat. In mammals, endogenous heat production increases markedly during gestation and lactation, and thus female mammals may be subject to greater thermal constraints on energy expenditure than males. Such constraints likely have important implications for behavior and population performance in a warming climate. 2. We used a mechanistic simulation model based on first...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of Idaho
  • United States Geological Survey
  • New Mexico State University
  • University of Kentucky
  • Humboldt State University
  • Harvard University
  • Washington State University
  • University of Oviedo
  • Icelandic Institute of Natural History
  • University of Washington